Looking for a bit of strategic advice here. I am planning to swap the optical drive on my new MBP with another HD.
The idea is to have application and system software on the primary disk (a 128GB SSD) and put the rest of heavy data on the second disk (500gb).

How would you tackle backups in such a way that I can image everything on third, external, bootable backup? I'm really confused and unsure if there any clever way to sort it out.

You'd partition the backup into two volumes, one for each source. Depending on how you're telling the system where the files are, you'd name the user volume the same as the source (eg "User Drive" or whatever), then schedule two Smart Updates.

Note that I'd probably create one account that had its home folder on the SSD, too, in case you need to do some things when the user volume was messed up or made incorrectly.